GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E3

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate AO353_25695 AO353_25695 AMP-binding protein

Query= SwissProt::Q3UNX5
         (580 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_25695 AO353_25695
           AMP-binding protein
          Length = 554

 Score =  273 bits (698), Expect = 1e-77
 Identities = 178/512 (34%), Positives = 277/512 (54%), Gaps = 27/512 (5%)

Query: 76  AFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACL 135
           A +W   +G    ++F +L   + +FAN L  A  +++GD+V  +LP+  E  +   A  
Sbjct: 45  ALFWEGRDGASATYTFSDLQDKAARFANFLL-AQGVKKGDKVAGLLPRNVELLIVVFATW 103

Query: 136 RTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHS 195
           R G V  P  T    K I +RL SS A  ++TD    P ++ VA          IV+   
Sbjct: 104 RIGAVYQPLFTAFGPKAIEHRLNSSGAAVVVTDAVNRPKLNDVA------DCPTIVTVGG 157

Query: 196 REGWGNLK-------EMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGL 248
            +G G ++       E+  Y++     +    D  + + FTSGTTGP K +     +  +
Sbjct: 158 PKGQGIVRGDFSFWAELPNYSAQCEPVLLDGEDPFL-LMFTSGTTGPSKALSVPLKAI-V 215

Query: 249 GLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQT 308
                 R  +DL   D  WN +D GWA   +  V  P + G  +  +  P F   S  + 
Sbjct: 216 AFQSYTRDAVDLRPEDAFWNVADPGWAYGIYFGVTGPLSMGHPITFYDGP-FTLESTCRV 274

Query: 309 LSKFPITVFCSAPTAYRMLVQ--NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDI 366
           ++K+ IT    +PTAYR+L+   ++ +      L+   SAGEP+NPEV+  +    G+ I
Sbjct: 275 INKYGITNLTGSPTAYRLLIAGGDEFARSIKGKLRIVSSAGEPLNPEVIRWFADNLGVVI 334

Query: 367 YEGYGQTETVLICGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVL 424
           ++ YGQTE  ++  N  G++  +  G+ G  SP   + +LDE    L  GQ G +A+   
Sbjct: 335 HDHYGQTELGMVLCNHHGLEHSVHVGAAGFASPGHRIVVLDEAYNELSVGQPGILAID-R 393

Query: 425 PERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGP 484
            + P   F  Y   P+K      G++Y++GD   ++ DG   FV RSDD+I +SGYR+GP
Sbjct: 394 TQSPMCWFAGYEGAPTKA---FVGNYYLSGDTVELNPDGSISFVGRSDDVITTSGYRVGP 450

Query: 485 FEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTT 544
           F+VESALIEHP++ E+AV+  PDP R E+VKAF+VL+  Y++    +L +E+++HV+K  
Sbjct: 451 FDVESALIEHPAVVEAAVIGKPDPERTELVKAFVVLSAQYRA--SPELAEELRQHVRKRL 508

Query: 545 APYKYPRKVEFIEELPKTVSGKVKRNELRKKE 576
           A + YPR++EF+ ELPKT SGK++R  LR +E
Sbjct: 509 AAHSYPREIEFVSELPKTPSGKLQRFILRNQE 540


Lambda     K      H
   0.319    0.134    0.416 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 750
Number of extensions: 48
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 580
Length of database: 554
Length adjustment: 36
Effective length of query: 544
Effective length of database: 518
Effective search space:   281792
Effective search space used:   281792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory